cljam.io.fastq
Functions to read and write the FASTQ format.
deserialize-casava-1_8-name
(deserialize-casava-1_8-name name)
Parses Casava1.8-style name of fastq read.
deserialize-casava-name
(deserialize-casava-name name)
Parses Casava-style name of fastq read.
deserialize-name
(deserialize-name name)
Tries parsing name of fastq read.
read-sequences
(read-sequences rdr)(read-sequences rdr opts)
Returns a lazy sequence of FASTQReads deserialized from given reader.
reader
(reader f)
Returns an open cljam.io.fastq.FASTQReader of f. Should be used inside
with-open to ensure the reader is properly closed.
serialize-casava-1_8-name
(serialize-casava-1_8-name {:keys [instrument run flowcell lane tile x y pair filtered control index]})
Encodes fastq name map to Casava1.8-style string.
serialize-casava-name
(serialize-casava-name {:keys [instrument lane tile x y index pair]})
Encodes fastq name map to Casava-style string.
serialize-name
(serialize-name name)
Tries encoding name of fastq read.
write-sequences
(write-sequences wtr sequences)(write-sequences wtr sequences opts)
Writes given sequence of reads to a FASTQ file.
writer
(writer f)
Returns an open cljam.io.fastq.FASTQWriter of f. Should be used inside
with-open to ensure the writer is properly closed.